This dashboard helps facilitate the CQI analyses VIHA E.C.R. (early cognitive recline) project.
By implementing plans for self-care activities with established clients, primary caregivers will see a mean score reduction of at least 4 points on the ECR after 4 months of self-care activities by Dec 1, 2018.
Report rendered by wibeasley at 2020-02-12, 21:08 -0600 in 11 seconds.
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand. But you’ll probably regret it.
| name | value |
|---|---|
| version | R version 3.6.2 (2019-12-12) |
| os | Ubuntu 19.10 |
| system | x86_64, linux-gnu |
| ui | X11 |
| language | (EN) |
| collate | en_US.UTF-8 |
| ctype | en_US.UTF-8 |
| tz | America/Chicago |
| date | 2020-02-12 |
| package | ondiskversion | loadedversion | attached | is_base | date | source |
|---|---|---|---|---|---|---|
| assertthat | 0.2.1 | 0.2.1 | FALSE | FALSE | 2019-03-21 | CRAN (R 3.6.1) |
| backports | 1.1.5 | 1.1.5 | FALSE | FALSE | 2019-10-02 | CRAN (R 3.6.1) |
| broom | 0.5.4 | 0.5.4 | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.2) |
| Cairo | 1.5.10 | 1.5-10 | FALSE | FALSE | 2019-03-28 | CRAN (R 3.6.1) |
| callr | 3.4.1 | 3.4.1 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| cli | 2.0.1 | 2.0.1 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| colorspace | 1.4.1 | 1.4-1 | FALSE | FALSE | 2019-03-18 | CRAN (R 3.6.1) |
| config | 0.3 | 0.3 | FALSE | FALSE | 2018-03-27 | CRAN (R 3.6.1) |
| crayon | 1.3.4 | 1.3.4 | FALSE | FALSE | 2017-09-16 | CRAN (R 3.6.1) |
| crosstalk | 1.0.0 | 1.0.0 | FALSE | FALSE | 2016-12-21 | CRAN (R 3.6.1) |
| data.table | 1.12.8 | 1.12.8 | FALSE | FALSE | 2019-12-09 | CRAN (R 3.6.1) |
| desc | 1.2.0 | 1.2.0 | FALSE | FALSE | 2018-05-01 | CRAN (R 3.6.1) |
| devtools | 2.2.1 | 2.2.1 | FALSE | FALSE | 2019-09-24 | CRAN (R 3.6.1) |
| digest | 0.6.23 | 0.6.23 | FALSE | FALSE | 2019-11-23 | CRAN (R 3.6.1) |
| dplyr | 0.8.4 | 0.8.4 | FALSE | FALSE | 2020-01-31 | CRAN (R 3.6.2) |
| DT | 0.12 | 0.12 | FALSE | FALSE | 2020-02-05 | CRAN (R 3.6.2) |
| ellipsis | 0.3.0 | 0.3.0 | FALSE | FALSE | 2019-09-20 | CRAN (R 3.6.1) |
| evaluate | 0.14 | 0.14 | FALSE | FALSE | 2019-05-28 | CRAN (R 3.6.1) |
| fansi | 0.4.1 | 0.4.1 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| farver | 2.0.3 | 2.0.3 | FALSE | FALSE | 2020-01-16 | CRAN (R 3.6.1) |
| fastmap | 1.0.1 | 1.0.1 | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.1) |
| flexdashboard | 0.5.1.1 | 0.5.1.1 | TRUE | FALSE | 2018-06-29 | CRAN (R 3.6.1) |
| fs | 1.3.1 | 1.3.1 | FALSE | FALSE | 2019-05-06 | CRAN (R 3.6.1) |
| generics | 0.0.2 | 0.0.2 | FALSE | FALSE | 2018-11-29 | CRAN (R 3.6.1) |
| ggplot2 | 3.2.1 | 3.2.1 | TRUE | FALSE | 2019-08-10 | CRAN (R 3.6.1) |
| glue | 1.3.1 | 1.3.1 | FALSE | FALSE | 2019-03-12 | CRAN (R 3.6.1) |
| gtable | 0.3.0 | 0.3.0 | FALSE | FALSE | 2019-03-25 | CRAN (R 3.6.1) |
| highr | 0.8 | 0.8 | FALSE | FALSE | 2019-03-20 | CRAN (R 3.6.1) |
| hms | 0.5.3 | 0.5.3 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| htmltools | 0.4.0 | 0.4.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| htmlwidgets | 1.5.1 | 1.5.1 | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.1) |
| httpuv | 1.5.2 | 1.5.2 | FALSE | FALSE | 2019-09-11 | CRAN (R 3.6.1) |
| httr | 1.4.1 | 1.4.1 | FALSE | FALSE | 2019-08-05 | CRAN (R 3.6.1) |
| import | 1.1.0 | 1.1.0 | FALSE | FALSE | 2015-06-22 | CRAN (R 3.6.1) |
| jsonlite | 1.6.1 | 1.6.1 | FALSE | FALSE | 2020-02-02 | CRAN (R 3.6.2) |
| kableExtra | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-03-16 | CRAN (R 3.6.1) |
| knitr | 1.28 | 1.28 | TRUE | FALSE | 2020-02-06 | CRAN (R 3.6.2) |
| labeling | 0.3 | 0.3 | FALSE | FALSE | 2014-08-23 | CRAN (R 3.6.1) |
| later | 1.0.0 | 1.0.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| lattice | 0.20.38 | 0.20-38 | FALSE | FALSE | 2018-11-04 | CRAN (R 3.6.1) |
| lazyeval | 0.2.2 | 0.2.2 | FALSE | FALSE | 2019-03-15 | CRAN (R 3.6.1) |
| lifecycle | 0.1.0 | 0.1.0 | FALSE | FALSE | 2019-08-01 | CRAN (R 3.6.1) |
| magrittr | 1.5 | 1.5 | FALSE | FALSE | 2014-11-22 | CRAN (R 3.6.1) |
| memoise | 1.1.0 | 1.1.0 | FALSE | FALSE | 2017-04-21 | CRAN (R 3.6.1) |
| mime | 0.9 | 0.9 | FALSE | FALSE | 2020-02-04 | CRAN (R 3.6.2) |
| munsell | 0.5.0 | 0.5.0 | FALSE | FALSE | 2018-06-12 | CRAN (R 3.6.1) |
| nlme | 3.1.144 | 3.1-144 | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.2) |
| pillar | 1.4.3 | 1.4.3 | FALSE | FALSE | 2019-12-20 | CRAN (R 3.6.1) |
| pkgbuild | 1.0.6 | 1.0.6 | FALSE | FALSE | 2019-10-09 | CRAN (R 3.6.1) |
| pkgconfig | 2.0.3 | 2.0.3 | FALSE | FALSE | 2019-09-22 | CRAN (R 3.6.1) |
| pkgload | 1.0.2 | 1.0.2 | FALSE | FALSE | 2018-10-29 | CRAN (R 3.6.1) |
| plotly | 4.9.1 | 4.9.1 | TRUE | FALSE | 2019-11-07 | CRAN (R 3.6.1) |
| prettyunits | 1.1.1 | 1.1.1 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| processx | 3.4.2 | 3.4.2 | FALSE | FALSE | 2020-02-09 | CRAN (R 3.6.2) |
| promises | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| ps | 1.3.0 | 1.3.0 | FALSE | FALSE | 2018-12-21 | CRAN (R 3.6.1) |
| purrr | 0.3.3 | 0.3.3 | FALSE | FALSE | 2019-10-18 | CRAN (R 3.6.1) |
| R6 | 2.4.1 | 2.4.1 | FALSE | FALSE | 2019-11-12 | CRAN (R 3.6.1) |
| RColorBrewer | 1.1.2 | 1.1-2 | FALSE | FALSE | 2014-12-07 | CRAN (R 3.6.1) |
| Rcpp | 1.0.3 | 1.0.3 | FALSE | FALSE | 2019-11-08 | CRAN (R 3.6.1) |
| readr | 1.3.1 | 1.3.1 | FALSE | FALSE | 2018-12-21 | CRAN (R 3.6.1) |
| remotes | 2.1.0 | 2.1.0 | FALSE | FALSE | 2019-06-24 | CRAN (R 3.6.1) |
| rlang | 0.4.4 | 0.4.4 | FALSE | FALSE | 2020-01-28 | CRAN (R 3.6.2) |
| rmarkdown | 2.1 | 2.1 | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.2) |
| rprojroot | 1.3.2 | 1.3-2 | FALSE | FALSE | 2018-01-03 | CRAN (R 3.6.1) |
| rstudioapi | 0.11 | 0.11 | FALSE | FALSE | 2020-02-07 | CRAN (R 3.6.2) |
| rvest | 0.3.5 | 0.3.5 | FALSE | FALSE | 2019-11-08 | CRAN (R 3.6.1) |
| scales | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-11-18 | CRAN (R 3.6.1) |
| sessioninfo | 1.1.1 | 1.1.1 | FALSE | FALSE | 2018-11-05 | CRAN (R 3.6.1) |
| shiny | 1.4.0 | 1.4.0 | FALSE | FALSE | 2019-10-10 | CRAN (R 3.6.1) |
| stringi | 1.4.5 | 1.4.5 | FALSE | FALSE | 2020-01-11 | CRAN (R 3.6.1) |
| stringr | 1.4.0 | 1.4.0 | FALSE | FALSE | 2019-02-10 | CRAN (R 3.6.1) |
| TabularManifest | 0.1.16.9003 | 0.1-16.9003 | FALSE | FALSE | 2019-11-16 | Github (Melinae/TabularManifest@4cbc21c) |
| testthat | 2.3.1 | 2.3.1 | FALSE | FALSE | 2019-12-01 | CRAN (R 3.6.1) |
| tibble | 2.1.3 | 2.1.3 | FALSE | FALSE | 2019-06-06 | CRAN (R 3.6.1) |
| tidyr | 1.0.2 | 1.0.2 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| tidyselect | 1.0.0 | 1.0.0 | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.2) |
| usethis | 1.5.1 | 1.5.1 | FALSE | FALSE | 2019-07-04 | CRAN (R 3.6.1) |
| vctrs | 0.2.2 | 0.2.2 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| viridisLite | 0.3.0 | 0.3.0 | FALSE | FALSE | 2018-02-01 | CRAN (R 3.6.1) |
| webshot | 0.5.2 | 0.5.2 | FALSE | FALSE | 2019-11-22 | CRAN (R 3.6.1) |
| withr | 2.1.2 | 2.1.2 | FALSE | FALSE | 2018-03-15 | CRAN (R 3.6.1) |
| xfun | 0.12 | 0.12 | FALSE | FALSE | 2020-01-13 | CRAN (R 3.6.1) |
| xml2 | 1.2.2 | 1.2.2 | FALSE | FALSE | 2019-08-09 | CRAN (R 3.6.1) |
| xtable | 1.8.4 | 1.8-4 | FALSE | FALSE | 2019-04-21 | CRAN (R 3.6.1) |
| yaml | 2.2.1 | 2.2.1 | FALSE | FALSE | 2020-02-01 | CRAN (R 3.6.2) |
---
title: "Cognitive Longitudinal Outcomes by Program --PDSA Cycle 3"
output:
flexdashboard::flex_dashboard:
social: [ "menu" ]
# orientation: rows
vertical_layout: fill
source_code: embed
css: ../common/style-cqi-cycle-4.css
# theme: cosmo
# theme: journal
---
```{r, echo=F, message=F}
# cat("Working directory: ", getwd())
library(knitr)
library(flexdashboard)
opts_knit$set(root.dir = '../../') #Don't combine this call with any other chunk -especially one that uses file paths.
```
```{r set-options, echo=F}
# cat("Working directory: ", getwd())
report_render_start_time <- Sys.time()
opts_chunk$set(
results = 'show',
comment = NA,
tidy = FALSE,
# dpi = 400,
# out.width = "650px", #This affects only the markdown, not the underlying png file. The height will be scaled appropriately.
fig.width = 6,
fig.height = 6,
fig.path = 'figure-dashboard-png/'
)
echo_chunks <- FALSE #Toggle for debugging.
message_chunks <- FALSE #Toggle for debugging.
options(width = 100) #So the output is 25% wider than the default.
read_chunk("./analysis/dashboard-1/dashboard-1.R") #This allows knitr to call chunks tagged in the underlying *.R file.
```
```{r load-sources, echo=echo_chunks, message=message_chunks}
```
```{r load-packages, echo=echo_chunks, message=message_chunks}
```
```{r declare-globals, echo=echo_chunks, results='show', message=message_chunks}
```
```{r rmd-specific, echo=echo_chunks, message=message_chunks}
# Put presentation-specific code in here. It doesn't call a chunk in the codebehind file.
# It should be rare (and used cautiously), but sometimes it makes sense to include code in Rmd
# that doesn't live in the codebehind R file.
```
```{r load-data, echo=echo_chunks, results='show', message=message_chunks}
```
```{r tweak-data, echo=echo_chunks, results='show', message=message_chunks}
```
Headline
=============================================
This dashboard helps facilitate the CQI analyses VIHA E.C.R. (early cognitive recline) project.
Overall {.tabset data-width=300}
---------------------------------------------
### Notes
1. The current report covers `r scales::comma(nrow(ds))` total subject-event records for `r dplyr::n_distinct(ds$county)` unique counties (`r paste(sort(unique(ds$county)), collapse=", ")`).
1. The year of collection ranges from `r min(ds$year, na.rm=T)` to `r max(ds$year, na.rm=T)`.
1. The selected county is `r county_name_focus` (id value `r county_id_focus`).
{.tabset}
---------------------------------------------
```{r headline-graph, echo=echo_chunks, results='asis', message=message_chunks}
```
Tables
=============================================
{.tabset}
---------------------------------------------
### Tables - County-Year
```{r tables-county-year, echo=echo_chunks, message=message_chunks}
```
### Tables - County
```{r tables-county, echo=echo_chunks, message=message_chunks}
```
### Tables - Annotation
```{r tables-annotation, echo=echo_chunks, message=message_chunks}
```
Spaghetti
=============================================
{.tabset}
---------------------------------------------
```{r spaghetti, echo=echo_chunks, message=message_chunks, results='asis', fig.height=10, fig.width=20}
```
Marginals
=============================================
{.tabset}
---------------------------------------------
```{r marginals, echo=echo_chunks, message=message_chunks, results='asis'}
```
Documentation
=============================================
{.tabset}
---------------------------------------------
### Explanation -Current PDSA
#### SMART Aim
By implementing plans for self-care activities with established clients, primary caregivers will see a mean score reduction of at least 4 points on the ECR after 4 months of self-care activities by Dec 1, 2018.
#### Measures
* **Outcome**: Parent Stress
* Pre- and Post- Parent Stress Scale score change
* **Process**: Completed Resiliency Plans
* *Numerator*: Count of clients who completed their designated self-care activity
* *Denominator*: Count of clients with a visist in a given week
* **Disruptor**: Cultural issues preventing participation, toxic stress, family catastrophe
#### Spaghetti Notes
* **To be added**:
* Post score plots
* Pre-post comparisons
* Splitting out new clients from old clients to see if differences are more or less prominent
* **Mean PSS Scores - Pre**:
* Each blue dot represents a single client's PSS score on the pre measure
* The orange dots (connected by the red line) represent the mean PSS score for all clients on a given week.
* Dot size is proportional to the number of clients who had a pre-PSS score.
* **Stress Activity - Success**:
* *Numerator*: Number of clients who indicated having completed their self-care activity
* *Denominator*: All clients who responded to the self-care question (Yes/No to self-care)
* *Dot size*: The dot size is proportional to the number of clients who responded to that question on a given week.
#### Resources
* [Current PDSA](https://docs.google.com/document/d/1IcwCCkr1EkoeBJpEKdF2v-E0gKI6wGacCv9oZU1CE7I/edit#) (This is accessible only to CQI participants.)
### Explanation -All CQI Dashboards
```{r, child = "../common/dashboard/documentation-all-dashboards-1.Rmd"}
```
### Glossary
```{r, child = "../common/dashboard/documentation-glossary-1.Rmd"}
```
### Tips
```{r, child = "../common/dashboard/documentation-tips-1.Rmd"}
```
### Config
```{r, child = "../common/dashboard/documentation-config-1.Rmd"}
```